SWIPE 2.0.9

torognes · Jan 21, 2014 · 262bfca · 262bfca
1 parent 934a2d9
commit 262bfca
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diff --git a/CHANGES b/CHANGES
@@ -1,3 +1,14 @@
+2014-01-21  Torbjorn Rognes  <[email protected]>
+	* Version 2.0.9
+	* Changed inline assembler syntax (adding register prefix) to
+	  adapt to the LLVM clang compiler on Mac
+	* Improved detection of CPU features (SSSE3 etc) and added
+	  alternative code for the search7 function for CPUs with 
+	  and without SSSE3
+	* Fixed an inconsistency in the counting of 'positives', i.e.
+	  similar but non-identical residues
+	* Added binaries for Mac, including an openmpi version
+
 2014-01-17  Torbjorn Rognes  <[email protected]>
 	* Version 2.0.8
 	* Removed a bug in computation of the score of alignments 

diff --git a/Linux/mpiswipe b/Linux/mpiswipe
diff --git a/Linux/swipe b/Linux/swipe
diff --git a/Mac/mpiswipe b/Mac/mpiswipe
diff --git a/Mac/swipe b/Mac/swipe
diff --git a/Makefile b/Makefile
@@ -30,7 +30,7 @@ MPI_LINK=`mpicxx --showme:link`
 COMMON=-g
 #COMMON=-pg -g
 
-COMPILEOPT=-Wall -mssse3
+COMPILEOPT=-Wall
 
 LIBS=-lpthread
 
@@ -53,7 +53,7 @@ clean :
 
 OBJS = database.o asnparse.o align.o matrices.o \
 	stats.o hits.o query.o \
-	search63.o search16.o search16s.o search7.o
+	search63.o search16.o search16s.o search7.o search7_ssse3.o
 
 DEPS = swipe.h Makefile
 
@@ -71,3 +71,5 @@ mpiswipe : mpiswipe.o $(OBJS)
 mpiswipe.o : swipe.cc $(DEPS)
 	$(CXX) $(CXXFLAGS) -DMPISWIPE $(MPI_COMPILE) -c -o $@ swipe.cc
 
+search7_ssse3.o : search7.cc $(DEPS)
+	$(CXX) -mssse3 $(CXXFLAGS) -DSWIPE_SSSE3 -c -o $@ search7.cc
diff --git a/Makefile.gnu b/Makefile.gnu
diff --git a/Makefile.intel b/Makefile.intel
diff --git a/README b/README
@@ -68,7 +68,9 @@ Usage: ./[mpi]swipe [OPTIONS]
   -o, --out=FILE             output file (stdout)
   -z, --dbsize=NUM           set effective database size (0)
 
-Defaults are indicated in parentheses in the option list above.
+Defaults are indicated in parentheses in the option list above. NUM means an
+integer, while REAL means a floating point number (possibly in scientific
+notation).
 
 Most features and options are similar and compatible with NCBI
 BLAST. 

diff --git a/hits.cc b/hits.cc
@@ -1070,8 +1070,11 @@ void count_align(long i,
 	char qs = q_seq[q_pos++];
 	char ds = d_seq[d_pos++];
 	if (qs == ds)
+	{
 	  (*identities)++;
-	if (score_matrix_63[32*qs+ds] > 0)
+	  (*positives)++;
+	}
+	else if (score_matrix_63[32*qs+ds] > 0)
 	  (*positives)++;
       }
     }